===============================
R CMD BUILD
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* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* preparing ‘CBN2Path’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘CBN2Path’ ...
** this is package ‘CBN2Path’ version ‘0.99.5’
** using staged installation
checking for gcc... gcc -std=gnu2x
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
checking for gsl-config... /usr/bin/gsl-config
checking if GSL version >= 2.5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c bcbn.c -o bcbn.o
bcbn.c: In function ‘bcbn_write_poset’:
bcbn.c:228:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
228 | for (j=0; j<n; j++)
| ^~~
bcbn.c:232:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
232 | fprintf(output, "0 0\n");
| ^~~~~~~
bcbn.c: In function ‘bcbn_is_equal_int_matrix’:
bcbn.c:332:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
332 | for (j=0; j<n; j++)
| ^~~
bcbn.c:336:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
336 | return 1;
| ^~~~~~
bcbn.c: In function ‘bcbn_free_lattice_children’:
bcbn.c:433:7: warning: unused variable ‘i’ [-Wunused-variable]
433 | int i;
| ^
bcbn.c: In function ‘bcbn_print_genotype’:
bcbn.c:641:7: warning: unused variable ‘i’ [-Wunused-variable]
641 | int i;
| ^
bcbn.c: In function ‘bcbn_bfs_order_ideals’:
bcbn.c:691:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
691 | for (j=0; j<lin_ext_size; j++)
| ^~~
bcbn.c:697:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
697 | if (! is_in) // add to linear extension:
| ^~
bcbn.c: In function ‘bcbn_hamming_distance’:
bcbn.c:794:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
794 | for(i=0; i<n; i++)
| ^~~
bcbn.c:801:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
801 | free(g);
| ^~~~
bcbn.c: In function ‘compute_all_cbn_prob’:
bcbn.c:1056:13: warning: unused variable ‘k’ [-Wunused-variable]
1056 | int i,j,c,k;
| ^
bcbn.c:1056:9: warning: unused variable ‘j’ [-Wunused-variable]
1056 | int i,j,c,k;
| ^
bcbn.c: In function ‘bcbn_reduce_to_cover_relations’:
bcbn.c:1212:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1212 | for (j=0; j<n; j++)
| ^~~
bcbn.c:1219:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1219 | while (empty(&q) == FALSE)
| ^~~~~
bcbn.c: In function ‘compute_likelihood’:
bcbn.c:1281:15: warning: unused variable ‘likelihood’ [-Wunused-variable]
1281 | long double likelihood, likelihood_d;
| ^~~~~~~~~~
bcbn.c: In function ‘relocate_theta_i’:
bcbn.c:1367:25: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
1367 | double alpha,beta,var,x;
| ^
bcbn.c:1367:21: warning: unused variable ‘var’ [-Wunused-variable]
1367 | double alpha,beta,var,x;
| ^~~
bcbn.c: In function ‘compute_theta_transition_prob’:
bcbn.c:1380:25: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
1380 | double alpha,beta,var,x;
| ^
bcbn.c:1380:21: warning: unused variable ‘var’ [-Wunused-variable]
1380 | double alpha,beta,var,x;
| ^~~
bcbn.c: In function ‘propose_new_cover_relation’:
bcbn.c:1449:11: warning: unused variable ‘k’ [-Wunused-variable]
1449 | int i,j,k,N_compatible,N_all_comp;
| ^
bcbn.c: In function ‘get_tp_for_new_cover_move’:
bcbn.c:1550:35: warning: unused variable ‘k’ [-Wunused-variable]
1550 | int i,j,N_all_comp,N_compatible,k;
| ^
bcbn.c:1550:22: warning: unused variable ‘N_compatible’ [-Wunused-variable]
1550 | int i,j,N_all_comp,N_compatible,k;
| ^~~~~~~~~~~~
bcbn.c:1550:11: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
1550 | int i,j,N_all_comp,N_compatible,k;
| ^~~~~~~~~~
bcbn.c: In function ‘relocate_epsilon’:
bcbn.c:1675:25: warning: unused variable ‘x’ [-Wunused-variable]
1675 | double alpha,beta,var,x;
| ^
bcbn.c:1675:21: warning: unused variable ‘var’ [-Wunused-variable]
1675 | double alpha,beta,var,x;
| ^~~
bcbn.c:1675:16: warning: unused variable ‘beta’ [-Wunused-variable]
1675 | double alpha,beta,var,x;
| ^~~~
bcbn.c:1675:10: warning: unused variable ‘alpha’ [-Wunused-variable]
1675 | double alpha,beta,var,x;
| ^~~~~
bcbn.c: In function ‘propose_new_bcbn_transitive_closure_relation’:
bcbn.c:1755:11: warning: unused variable ‘k’ [-Wunused-variable]
1755 | int i,j,k,N_compatible,N_all_comp;
| ^
bcbn.c: In function ‘propose_delete_bcbn_transitive_closure_relation’:
bcbn.c:1878:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
1878 | int i,j,k,N_compatible,N_all_comp;
| ^~~~~~~~~~
bcbn.c:1878:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
1878 | int i,j,k,N_compatible,N_all_comp;
| ^~~~~~~~~~~~
bcbn.c:1878:11: warning: unused variable ‘k’ [-Wunused-variable]
1878 | int i,j,k,N_compatible,N_all_comp;
| ^
bcbn.c: In function ‘get_tp_for_delete_bcbn_transitive_closure_relation_move’:
bcbn.c:1957:7: warning: unused variable ‘c’ [-Wunused-variable]
1957 | int c = 0;
| ^
bcbn.c:1946:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
1946 | int i,j,k,N_compatible,N_all_comp;
| ^~~~~~~~~~
bcbn.c:1946:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
1946 | int i,j,k,N_compatible,N_all_comp;
| ^~~~~~~~~~~~
bcbn.c:1946:11: warning: unused variable ‘k’ [-Wunused-variable]
1946 | int i,j,k,N_compatible,N_all_comp;
| ^
bcbn.c: In function ‘get_tp_for_new_bcbn_transitive_closure_relation_move’:
bcbn.c:2008:7: warning: unused variable ‘c’ [-Wunused-variable]
2008 | int c = 0;
| ^
bcbn.c:1997:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
1997 | int i,j,k,N_compatible,N_all_comp;
| ^~~~~~~~~~
bcbn.c:1997:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
1997 | int i,j,k,N_compatible,N_all_comp;
| ^~~~~~~~~~~~
bcbn.c:1997:11: warning: unused variable ‘k’ [-Wunused-variable]
1997 | int i,j,k,N_compatible,N_all_comp;
| ^
bcbn.c: In function ‘start_Exp_theta_MH’:
bcbn.c:2362:7: warning: unused variable ‘accepted’ [-Wunused-variable]
2362 | int accepted = 0;
| ^~~~~~~~
bcbn.c:2358:9: warning: unused variable ‘j’ [-Wunused-variable]
2358 | int i,j,k = 0;
| ^
bcbn.c:2358:7: warning: unused variable ‘i’ [-Wunused-variable]
2358 | int i,j,k = 0;
| ^
bcbn.c: In function ‘run_MH_sampler’:
bcbn.c:2620:22: warning: unused variable ‘MH_ratio’ [-Wunused-variable]
2620 | long double alpha, MH_ratio;
| ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ctcbn.c -o ctcbn.o
In file included from ctcbn.c:3:
ct-cbn.h: In function ‘print_int_array’:
ct-cbn.h:184:7: warning: unused variable ‘j’ [-Wunused-variable]
184 | int j;
| ^
ct-cbn.h: In function ‘write_poset’:
ct-cbn.h:274:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
274 | for (j=1; j<=n; j++)
| ^~~
ct-cbn.h:278:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
278 | fprintf(output, "0\n");
| ^~~~~~~
ct-cbn.h: In function ‘print_genotype’:
ct-cbn.h:803:7: warning: unused variable ‘i’ [-Wunused-variable]
803 | int i;
| ^
ct-cbn.h: In function ‘bfs_order_ideals’:
ct-cbn.h:853:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
853 | for (j=0; j<lin_ext_size; j++)
| ^~~
ct-cbn.h:859:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
859 | if (! is_in) // add to linear extension:
| ^~
ct-cbn.h: In function ‘hamming_distance’:
ct-cbn.h:956:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
956 | for(i=0; i<n; i++)
| ^~~
ct-cbn.h:963:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
963 | free(g);
| ^~~~
ct-cbn.h: In function ‘is_after’:
ct-cbn.h:1198:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1198 | for ( a=0; a<=M->n; a++ )
| ^~~
ct-cbn.h:1201:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1201 | return 1;
| ^~~~~~
ct-cbn.h: In function ‘is_strict_after’:
ct-cbn.h:1211:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1211 | for ( a=0; a<=M->n; a++ )
| ^~~
ct-cbn.h:1214:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1214 | return 1;
| ^~~~~~
ct-cbn.h: In function ‘compute_all_exp’:
ct-cbn.h:1283: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1283 | #pragma omp parallel for private(i,c,k,j,g, all_pred_in_k, pred,l)
|
ct-cbn.h:1318:11: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1318 | for (l = 0; l < m; l++)
| ^~~
ct-cbn.h:1346:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1346 | Exp[pos][i] = censexp[pos][i][m-1];
| ^~~
ct-cbn.h: In function ‘EM_epsilon’:
ct-cbn.h:1440:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1440 | for(i = 1; i < m; i++)
| ^~~
ct-cbn.h:1447:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1447 | loglik_new += log (prob_tmp) * D[k].count;
| ^~~~~~~~~~
ct-cbn.h: In function ‘compute_loglik’:
ct-cbn.h:1471:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1471 | for(i = 1; i < m; i++)
| ^~~
ct-cbn.h:1477:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1477 | loglik[k] = log (prob_tmp) ;
| ^~~~~~
ct-cbn.h: In function ‘MLE’:
ct-cbn.h:1833:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1833 | for (k=0; k<N_u; k++)
| ^~~
ct-cbn.h:1839:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1839 | lambda[i] = (double) N / sum;
| ^~~~~~
ct-cbn.h: In function ‘EM’:
ct-cbn.h:1920:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1920 | for (k=0; k<N_u; k++)
| ^~~
ct-cbn.h:1939:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1939 | if (verbose)
| ^~
ct-cbn.h: In function ‘violation_map’:
ct-cbn.h:2488:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
2488 | for (i=1; i<=n; i++)
| ^~~
ct-cbn.h:2502:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
2502 | qsort(V, idx, sizeof(int *), compare_violation_pairs); // small violators first
| ^~~~~
ct-cbn.h: In function ‘reduce_to_cover_relations’:
ct-cbn.h:2524:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
2524 | for (j=1; j<=n; j++)
| ^~~
ct-cbn.h:2531:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
2531 | while (empty(&q) == FALSE)
| ^~~~~
ct-cbn.h: In function ‘try_edge’:
ct-cbn.h:2741:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
2741 | for(j=0;j<n*n;j++)
| ^~~
ct-cbn.h:2744:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
2744 | R4[i] = c;
| ^~
ct-cbn.h:2784:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
2784 | for(i=1;i<n+1;i++)
| ^~~
ct-cbn.h:2790:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
2790 | if(c == 1)
| ^~
ct-cbn.h:2943:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
2943 | for(i=1;i<n+1;i++)
| ^~~
ct-cbn.h:2949:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
2949 | if(c == 1)
| ^~
ct-cbn.h:2721:17: warning: variable ‘alpha_new’ set but not used [-Wunused-but-set-variable]
2721 | double alpha, alpha_new;
| ^~~~~~~~~
ct-cbn.h: In function ‘local_search’:
ct-cbn.h:3134:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
3134 | for(j=1;j<=M->n;j++)
| ^~~
ct-cbn.h:3161:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
3161 | print_double_matrix(loglik_next, M->n, M->n);
| ^~~~~~~~~~~~~~~~~~~
ct-cbn.h: In function ‘is_equal_int_matrix’:
ct-cbn.h:3196:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
3196 | for (j=0; j<n; j++)
| ^~~
ct-cbn.h:3200:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
3200 | return 1;
| ^~~~~~
ct-cbn.h: In function ‘ML_path’:
ct-cbn.h:3305:7: warning: variable ‘mut_next’ set but not used [-Wunused-but-set-variable]
3305 | int mut_next, index_next;
| ^~~~~~~~
ctcbn.c: In function ‘ctcbn_’:
ctcbn.c:234:11: error: format not a string literal and no format arguments [-Werror=format-security]
234 | fprintf(summaryFile, select_poset(k, epsilon, &M, lambda, D, N_u, R, LEARN_BOTH, 1));
| ^~~~~~~
ctcbn.c:88:7: warning: unused variable ‘c’ [-Wunused-variable]
88 | int c = 0;
| ^
ctcbn.c:84:7: warning: unused variable ‘GPS’ [-Wunused-variable]
84 | int GPS = 0;
| ^~~
ctcbn.c:79:7: warning: unused variable ‘verbose’ [-Wunused-variable]
79 | int verbose = 0;
| ^~~~~~~
ctcbn.c: In function ‘hcbn_’:
ctcbn.c:320:7: warning: unused variable ‘c’ [-Wunused-variable]
320 | int c = 0;
| ^
ctcbn.c:315:7: warning: variable ‘N_iter’ set but not used [-Wunused-but-set-variable]
315 | int N_iter = 0;
| ^~~~~~
ctcbn.c:314:10: warning: unused variable ‘T’ [-Wunused-variable]
314 | double T = REAL(temp)[0];
| ^
ctcbn.c:309:7: warning: unused variable ‘t_flag’ [-Wunused-variable]
309 | int t_flag = 1;
| ^~~~~~
ctcbn.c:307:7: warning: unused variable ‘l_flag’ [-Wunused-variable]
307 | int l_flag = 0;
| ^~~~~~
ctcbn.c:306:7: warning: unused variable ‘gps_flag’ [-Wunused-variable]
306 | int gps_flag = 0;
| ^~~~~~~~
ctcbn.c:305:7: warning: variable ‘e_flag’ set but not used [-Wunused-but-set-variable]
305 | int e_flag = 0;
| ^~~~~~
ctcbn.c:304:7: warning: unused variable ‘f_flag’ [-Wunused-variable]
304 | int f_flag = 0;
| ^~~~~~
ctcbn.c:303:7: warning: unused variable ‘error_flag’ [-Wunused-variable]
303 | int error_flag = 0;
| ^~~~~~~~~~
ctcbn.c:469:10: warning: ‘rOutput’ may be used uninitialized [-Wmaybe-uninitialized]
469 | return char_to_sexp(rOutput);
| ^~~~~~~~~~~~~~~~~~~~~
ctcbn.c:321:9: note: ‘rOutput’ was declared here
321 | char* rOutput;
| ^~~~~~~
cc1: some warnings being treated as errors
make: *** [/home/biocbuild/bbs-3.22-bioc/R/etc/Makeconf:202: ctcbn.o] Error 1
ERROR: compilation failed for package ‘CBN2Path’
* removing ‘/tmp/RtmpqiJVcs/Rinst6f2e47619be76/CBN2Path’
-----------------------------------
ERROR: package installation failed